Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: "" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.008917/0.008917, allocations: 103.5 kB / 15.73 MB, free: 6.043 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001642/0.001642, allocations: 201.2 kB / 16.68 MB, free: 5.98 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.535/1.535, allocations: 222.9 MB / 240.4 MB, free: 15.16 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1102/0.1102, allocations: 12.28 MB / 302.8 MB, free: 3.227 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001268/0.001268, allocations: 61.88 kB / 419.5 MB, free: 17.53 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1401/0.1413, allocations: 52.09 MB / 471.6 MB, free: 13.45 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.008755/0.1502, allocations: 4.305 MB / 475.9 MB, free: 9.125 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0009883/0.1512, allocations: 299.3 kB / 476.2 MB, free: 8.832 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003262/0.1516, allocations: 19.94 kB / 476.2 MB, free: 8.812 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002486/0.1518, allocations: 55.55 kB / 476.3 MB, free: 8.758 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004226/0.1524, allocations: 71.3 kB / 476.4 MB, free: 8.688 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003455/0.1527, allocations: 63.89 kB / 476.4 MB, free: 8.625 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0006027/0.1534, allocations: 303.2 kB / 476.7 MB, free: 8.328 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004548/0.1538, allocations: 156.5 kB / 476.9 MB, free: 8.172 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002153/0.154, allocations: 127.6 kB / 477 MB, free: 8.047 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002863/0.1543, allocations: 159.3 kB / 477.1 MB, free: 7.891 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 9.406e-05/0.1544, allocations: 32 kB / 477.2 MB, free: 7.859 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 8.631e-05/0.1545, allocations: 32 kB / 477.2 MB, free: 7.828 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.662e-05/0.1546, allocations: 75.7 kB / 477.3 MB, free: 7.754 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002067/0.1548, allocations: 163.2 kB / 477.4 MB, free: 7.594 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0004976/0.1553, allocations: 362.4 kB / 477.8 MB, free: 7.242 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.584e-06/0.1554, allocations: 0 / 477.8 MB, free: 7.242 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.634e-06/0.1554, allocations: 4 kB / 477.8 MB, free: 7.238 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 2.005e-05/0.1554, allocations: 4 kB / 477.8 MB, free: 7.234 MB / 350.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.001407/0.1568, allocations: 0.601 MB / 478.4 MB, free: 6.582 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 6.077e-05/0.1569, allocations: 8.031 kB / 478.4 MB, free: 6.574 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001341/0.157, allocations: 78.7 kB / 478.5 MB, free: 6.488 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.692e-05/0.1571, allocations: 36.47 kB / 478.5 MB, free: 6.453 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002219/0.1573, allocations: 203.9 kB / 478.7 MB, free: 6.215 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.77e-05/0.1574, allocations: 25.38 kB / 478.8 MB, free: 6.191 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.375e-05/0.1575, allocations: 40.38 kB / 478.8 MB, free: 6.152 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006384/0.1581, allocations: 311.1 kB / 479.1 MB, free: 5.844 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.451e-05/0.1582, allocations: 3.938 kB / 479.1 MB, free: 5.84 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.156e-05/0.1582, allocations: 19.98 kB / 479.1 MB, free: 5.82 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.193e-05/0.1582, allocations: 15.94 kB / 479.1 MB, free: 5.805 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005007/0.1587, allocations: 239.9 kB / 479.4 MB, free: 5.566 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002251/0.161, allocations: 1.027 MB / 480.4 MB, free: 4.488 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003835/0.1614, allocations: 188.6 kB / 480.6 MB, free: 4.297 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001926/0.1616, allocations: 124.8 kB / 480.7 MB, free: 4.172 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.993e-05/0.1616, allocations: 4 kB / 480.7 MB, free: 4.168 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.901e-05/0.1617, allocations: 38.88 kB / 480.7 MB, free: 4.121 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.724e-06/0.1617, allocations: 3.938 kB / 480.7 MB, free: 4.117 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.002336/0.164, allocations: 0.898 MB / 481.6 MB, free: 3.168 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.031e-05/0.1641, allocations: 59.34 kB / 481.7 MB, free: 3.098 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000191/0.1643, allocations: 163.3 kB / 481.9 MB, free: 2.922 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.424e-05/0.1644, allocations: 33.7 kB / 481.9 MB, free: 2.883 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001565/0.1645, allocations: 215.4 kB / 482.1 MB, free: 2.668 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.136e-05/0.1646, allocations: 98.58 kB / 482.2 MB, free: 2.57 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001268/0.1647, allocations: 65.61 kB / 482.3 MB, free: 2.5 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001881/0.1649, allocations: 334.8 kB / 482.6 MB, free: 2.164 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001523/0.1651, allocations: 80.34 kB / 482.7 MB, free: 2.082 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002566/0.1654, allocations: 194.4 kB / 482.9 MB, free: 1.844 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003308/0.1687, allocations: 0.8143 MB / 483.7 MB, free: 0.9766 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.588e-06/0.1687, allocations: 0 / 483.7 MB, free: 0.9766 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0006316/0.1693, allocations: 345.1 kB / 484 MB, free: 0.6328 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.009e-05/0.1694, allocations: 8 kB / 484 MB, free: 0.625 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.697e-05/0.1694, allocations: 7.984 kB / 484 MB, free: 0.6172 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.61e-05/0.1694, allocations: 4 kB / 484 MB, free: 0.6133 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003286/0.1698, allocations: 84.31 kB / 484.1 MB, free: 0.5312 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.645e-05/0.1698, allocations: 11.94 kB / 484.1 MB, free: 0.5195 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000172/0.17, allocations: 8 kB / 484.1 MB, free: 0.5117 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.8e-05/0.17, allocations: 16 kB / 484.1 MB, free: 0.4961 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         X.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         M.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         C.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 16
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (46):
 * Single equations (assignments): 46
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0003768/0.1704, allocations: 183.4 kB / 484.3 MB, free: 316 kB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.53e-05/0.1705, allocations: 15.81 kB / 484.3 MB, free: 300 kB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 9.38e-05/0.1706, allocations: 33.86 kB / 484.4 MB, free: 264 kB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.272e-06/0.1706, allocations: 4 kB / 484.4 MB, free: 260 kB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.107e-06/0.1706, allocations: 0 / 484.4 MB, free: 260 kB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.27e-06/0.1706, allocations: 0 / 484.4 MB, free: 260 kB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000636/0.1713, allocations: 357.5 kB / 484.7 MB, free: 15.85 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.388e-06/0.1713, allocations: 0 / 484.7 MB, free: 15.85 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002751/0.1716, allocations: 47.97 kB / 484.8 MB, free: 15.8 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.579e-06/0.1716, allocations: 4 kB / 484.8 MB, free: 15.8 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.448e-05/0.1716, allocations: 8 kB / 484.8 MB, free: 15.79 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.479e-06/0.1716, allocations: 0 / 484.8 MB, free: 15.79 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.337e-06/0.1716, allocations: 7.938 kB / 484.8 MB, free: 15.79 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005924/0.1722, allocations: 431.2 kB / 485.2 MB, free: 15.35 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.055e-05/0.1723, allocations: 88.92 kB / 485.3 MB, free: 15.25 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.991e-05/0.1723, allocations: 12.05 kB / 485.3 MB, free: 15.23 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001416/0.1725, allocations: 4 kB / 485.3 MB, free: 15.23 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.464e-05/0.1725, allocations: 27.91 kB / 485.3 MB, free: 15.2 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.251e-05/0.1726, allocations: 4 kB / 485.4 MB, free: 15.2 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0001027/0.1727, allocations: 116 kB / 485.5 MB, free: 15.09 MB / 366.1 MB
Notification: Performance of sort global known variables: time 2.4e-07/0.1727, allocations: 0 / 485.5 MB, free: 15.09 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.0004135/0.1731, allocations: 64 kB / 485.5 MB, free: 15.02 MB / 366.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (26):
 * Single equations (assignments): 26
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.001078/0.1742, allocations: 0.9659 MB / 486.5 MB, free: 14.03 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004801/0.1747, allocations: 243.7 kB / 486.7 MB, free: 13.79 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.817e-06/0.1747, allocations: 3.938 kB / 486.7 MB, free: 13.79 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001637/0.1749, allocations: 107.8 kB / 486.8 MB, free: 13.68 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003816/0.1753, allocations: 27.45 kB / 486.9 MB, free: 13.66 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004122/0.1794, allocations: 2.746 MB / 489.6 MB, free: 10.74 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004939/0.1799, allocations: 0.7675 MB / 490.4 MB, free: 9.949 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 0.0001238/0.18, allocations: 25.94 kB / 490.4 MB, free: 9.926 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001596/0.1802, allocations: 95.39 kB / 490.5 MB, free: 9.836 MB / 366.1 MB
Notification: Performance of SimCode: time 1.273e-06/0.1802, allocations: 0 / 490.5 MB, free: 9.836 MB / 366.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.03664/0.2169, allocations: 4.414 MB / 494.9 MB, free: 5.484 MB / 366.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 8.752/8.969, allocations: 13.41 kB / 494.9 MB, free: 5.473 MB / 366.1 MB
(rm -f BioChem_BioChem.Examples.GMO.cell.pipe ; mkfifo BioChem_BioChem.Examples.GMO.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.GMO.cell.pipe >> ../files/BioChem_BioChem.Examples.GMO.cell.sim & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator  --tempDir=temp_BioChem_BioChem_Examples_GMO_cell_fmu --startTime=0 --stopTime=100 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_GMO_cell.fmu > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)